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why enzyme? if its any enzyme, why not any gene? loosening up in this regard might make it easier.
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shigetaFeb 27 '13 at 14:03

What level of similarity would be acceptable? What do you mean by "isn't common"? What exactly do you want to do?
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terdonFeb 27 '13 at 16:05

1

Do you just need a unique protein/DNA sequence, and how unique and how long does it need to be? What exactly is the aim of your project? A common problem is that protein/enzyme names may not be identical between species, but their functional domains and/or sequences could very well be, since many processes of life are conserved from one species to the next.
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MattDMoFeb 27 '13 at 19:50

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This question would fly rather well if you asked 'how can i find genes that are unique for C elegans?' Is that what you want to know?
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shigetaFeb 28 '13 at 21:27

Largely the authors focused on comparisons of Arabidopsis, Chlamydomonas and Human genomes, but they did also include C. elegans for comparisons with at least Chlamydomonas (Summarized in Table 1). Even if they do not give you exactly what you need, you could apply their methods for your particular project.

One way to approach this is to use one of the protein database clusterings available.

Researchers have taken huge protein databases, like UniProt, which basically catalog all known protein sequences regardless of species and clustered the proteins by sequence. The results provide many interesting insights about protein families, but more importantly they are well-fitted for your problem. A cluster would be a set of sequences that are similar to each other but are relatively different from all other known proteins. So, essentially you would be interested in a cluster that is only has c elegans proteins.

I went ahead and used ProtoNet, which is one such tool, and searched for such a c elegans cluster. I found two potential clusters: 4375747 and 4430980, which have mainly c elegans proteins.

Disclaimer: I have been involved in the past in the development of ProtoNet.